Human Genetics Exam 3 Study Guide
If the DNA non-coding (template) strand is 5' - ACG TAG CCA GGT - 3' what is the mRNA sequence transcribed?
- 3' - UGC AUC GGU CCA - 5' - or 5' - ACC UGG CUA CGU - 3'
How many amino acids are in the polypeptide encoded by this gene? 3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3'
- 6 - The start codon is #1 and there are 5 more before a stop codon is encountered.
Based on the gene and protein sequences that follow, what type of mutation has occurred? Normal gene DNA: ATG GCC GGC CCG AAA GAG ACC Mutated gene DNA : ATG GCC GGC CCA GAG ACC Normal protein: Met-Ala-Gly-Pro-Lys-Glu-Thr Mutated protein: Met-Ala-Gly-Pro-Glu-Asp
- A 3 base pair deletion occurred between nucleotides 12 and 14 resulting in the deletion of three nucleotides, resulting in one codon being altered (but it encodes the same amino acid), and one codon being deleted - The deletion did not cause a frameshift mutation
How can a TNRE in the coding region of the Huntington gene cause the Huntington disease phenotype?
- A CAG TNRE in the coding region of the Huntington gene results in additional glutamine amino acids in the resulting polypeptide - If the number of glutamine amino acids gets above a critical number, the long glutamine tract causes the protein to form aggregates, which disrupts the normal functioning of the protein.
How does a TNRE in the 5' untranslated region of the FMR1 gene cause the Fragile-X syndrome phenotype?
- A CCG TNRE in the 5' UTR of the FMR1 gene introduces a CpG island in the 5' region of the gene - The DNA subsequently gets methylated resulting in gene silencing
Based on the gene and protein sequences that follow, what type of mutation has occurred? Normal gene DNA: ATG GCC GGC CCG AAA GAG ACC Mutated gene DNA : ATG GCC GGC ACC GAA AGA GAC C Normal protein: Met-Ala-Gly-Pro-Lys-Glu-Thr Mutated protein: Met-Ala-Gly-Thr-Glu-Arg-Asp
- A base was inserted between nucleotides 9 and 10 - caused a frameshift mutation
What is a codon? Is a codon specified by DNA, mRNA or tRNA? Are codons read from 5' - 3' or 3' - 5'? How many nucleotides make up a codon?
- A codon is a sequence of 3 consecutive nucleotides that corresponds to a specific amino acid or an end to translation - Codon sequences are in DNA and mRNA, but the codon table specifies the mRNA codon sequence - Codons are read from 5' - 3'
What are the base pairing rules between DNA and RNA during transcription?
- A in DNA pairs with U in RNA - T in DNA pairs with A in RNA - G in DNA pairs with C in RNA - C in DNA pairs with G in RNA
How can a mutation in the promoter region of a gene, or a regulatory region of a gene, affect the amount of gene product produced?
- A mutation in the promoter region may affect the ability of RNA polymerase and general transcription factors to bind and initiate transcription - A mutation in regulatory sequences may affect the ability of regulatory transcription factors (enhancers and repressors) to bind, thereby altering the rate of transcription
What is a gene? What 2 types of functional products do genes encode?
- A segment of DNA that encodes a functional product - either a polypeptide or a functional RNA molecule
What effect to activators have on gene expression? What sequence do activators bind to?
- Activators promote gene transcription - Activators bind to enhancer sequences in DNA
What is RNA editing? What is the result of RNA editing?
- After transcription, one base is converted to a different base - RNA editing alters the structure and/or properties of the resulting polypeptide
An RNA transcript has the sequence below. What is the sequence of the template and coding DNA strands from which the transcript was produced? On which side (5' or 3') of the template strand is the promoter located? mRNA sequence: 5' - GGC AUG CAU UAC GGC AUC ACA CUA GGG AUC - 3'
- Coding strand: 5' - GGC ATG CAT TAC GGC ATC ACA CTA GGG ATC - 3' - Template strand: 3' - CCG TAC GTA ATG CCG TAG TGT GAT CCC TAG - 5' - the promoter is located at the 3' end of the template strand
Explain how pyrimidine dimers can cause mutation during DNA replication.
- Cytosine bases in a pyrimidine dimer are more prone to deamination to form uracil versus cytosine bases that are not in a dimer, which can result in a base substitution event during DNA replication - the normal replicative DNA polymerases (delta and epsilon) cannot replicate over bulky pyrimidine dimers that distort of the DNA double helix - If the dimer is not repaired prior to DNA replication, translesion bypass polymerases can be used to replicate over the lesion and the translesion bypass polymerases have a higher error rate
When does DNA replication take place?
- DNA must be replicated every time a cell divides to produce new cells - Cell division takes place during growth and development of an organism, to repair damaged cells, to produce gametes, and to replace cells that are renewed daily -S phase of the cell cycle
What are introns and exons?
- Exons are coding regions that are translated to produce an amino acid sequence - Introns are non-coding intervening regions that do not encode amino acids
What are general transcription factors (GTFs)? Do all genes transcribed by the same RNA polymerase require the same set of GTFs or do different genes use different GTFs?
- GTFs are transcription factors that required for transcription initiation by RNA polymerase - all genes transcribed by the same RNA polymerase require the same set of GTFs - all genes transcribed by RNA pol II require the same set of GTFs for transcription initiation - the GTFs bind to the promoter region and recruit RNA pol to the promoter
How can depurination introduce a base substitution during DNA replication?
- If the empty site is not repaired prior to DNA replication, DNA polymerase can add any of the four bases opposite the empty site - If DNA polymerase adds a base that is not the original base then a base substitution event occurs.
What does it mean to say that the genetic code is degenerate?
- It means the same amino acid can be specified by more than one codon - There are only 20 standard amino acids, but there are 61 different codons that specify amino acids
How does the addition or deletion of a number of nucleotides divisible by three effect the resulting polypeptide?
- It results in the addition or deletion of an amino acid, but it does not alter the reading frame of the downstream codons - Depending on the location of the added/deleted nucleotides (i.e., if it doesn't occur nicely between existing codons), they may also disrupt an existing codon
What effect does methylation of CpG islands have on gene expression, and why does it have that effect?
- Methylation of CpG islands is associated with gene silencing - Methyl groups may directly inhibit the binding of activators to enhancers, or methyl groups may attract methyl binding proteins that interact with other proteins, which then promote gene silencing
Does RNA polymerase require a primer? In which direction does RNA polymerase synthesize a strand of mRNA ?
- RNA polymerase does not require a primer - RNA polymerase synthesizes an mRNA strand in the 5'-3' direction
Which enzyme transcribes DNA to RNA? How many different types of RNA polymerase are there in humans?
- RNA polymerase transcribes DNA to RNA - humans have 3 RNA polymerase enzymes - RNA polymerase II transcribes all polypeptide encoding genes to mRNA - RNA pol I and RNA pol III transcribe genes encoding functional RNA molecules
explain how ROS can react with DNA to introduce a base substitution event during DNA replication.
- ROS are produced during normal cellular processes in the body, but ROS can also result from exposure to certain environmental agents - ROS can react with DNA to alter the structure of DNA bases - The altered bases do not follow the same base pairing rules during DNA replication
What are regulatory transcription factors (RTFs)? Do all genes transcribed by the same RNA polymerase require the same set of RTFs, or do different genes use different RTFs?
- Regulatory transcription factors regulate transcription level - Genes transcribed by a particular RNA polymerase are controlled by different combinations of regulatory transcription factors. For example, all genes transcribed by RNA pol II require the same set of general transcription factors, but different genes are controlled by different sets of regulatory transcription factors because different genes are transcribed at different rates, and different sets of genes are expressed in different cell types, during different stages of development, and under different environmental conditions.
What effect do repressors have on gene expression? What sequence to repressors bind to?
- Repressors inhibit gene transcription - Repressors bind to silencer sequences in DNA
How many subunits does a ribosome have, and which two types of macromolecule are ribosomes composed of?
- Ribosomes have a small 40S subunit and a large 60S subunit - The subunits are composed of ribosomal RNA (rRNA) molecules and proteins
Which codons are synonymous with CUU?
- Synonymous codons are those that specify the same amino acid - Non-synonymous codons specify different amino acids - UUA, UUG, CUC, CUA, CUG are all synonymous with CUU
What are the 5' and 3' untranslated regions?
- The 5' untranslated region (UTR) is a region upstream from (before) the translation start site, and it does not get translated to amino acid - The 3' UTR is a region downstream from (after) the stop codon, and it does not get translated to amino acid - The UTR is a common location where regulatory proteins associate with the mRNA
Alkylating agents are chemicals that add alkyl groups to bases. Explain how an alkylated base can result in a base substitution event during DNA replication.
- The alkylated base does not follow the same base pairing rules as the original base during DNA replication - a base substitution event will occur if the alkylated base is not repaired prior to DNA replication
explain how deamination and tautomeric shift result in a base substitution event during DNA replication.
- The bases have a common form and a rare form. Bases are held in their common form in the DNA double helix due to hydrogen bonding with a base on the other strand. When DNA strands are separated for DNA replication tautomeric shift can occur - The two tautomers of a base do not follow the same base pairing rules during DNA replication, so a base substitution event occurs if a base undergoes tautomeric shift to its rare form just prior to DNA replication.
The diagram below depicts a gene and shows the positions that encode translational start and stop codons. Which strand (top or bottom) is the template strand for this gene? 3'------------AAT--------------------GTA------------5' 5'------------TTA--------------------CAT-------------3'
- The bottom strand is the template strand because it will be transcribed to an mRNA with the start codon, AUG, at the 5' end and the stop codon, UAA, at the 3' end - The top strand is the coding strand because it contains a start codon and a stop codon
What is the histone code? What effect does acetylation of histone tails have on chromatin structure and gene expression? What effect does methylation and phosphorylation of histone tails have on chromatin structure and gene expression?
- The histone code refers to the pattern of histone tail modifications: acetyl, methyl, and phosphate groups can be added to amino acids in histone tails, and the specific pattern of chemical groups added affects chromatin structure - acetylation causes a more open chromatin structure, which promotes gene expression by making DNA more accessible - Methylation and phosphorylation is associated with gene expression or gene silencing depending on 1) the amino acids that are modified and 2) the number of chemical groups attached at a particular position
If the DNA template strand is 5' - TCA ACG TAG CCA GGT CAT- 3' what is the amino acid sequence of the polypeptide encoded by the gene? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?
- The mRNA is: 5' - AUG ACC UGG CUA CGU UGA - 3' - The resulting polypeptide is therefore: Met-Thr-Trp-Leu-Arg - Met is at the N-terminus and Arg is at the C-terminus
If the DNA coding strand is 5' - ATG ACG TCG CCA GGT TGA- 3' what is the amino acid sequence of the polypeptide produced by the gene? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?
- The mRNA is: 5' - AUG ACG UCG CCA GGU UGA - 3' - The resulting polypeptide is therefore: Met-Thr-Ser-Pro-Gly - Met is at the N-terminus and Gly is at the C-terminus
Explain how one determines the spontaneous mutation rate and how one determines if a chemical agent is a likely mutagen in the Ames test.
- The number of colonies on the control plate represents the spontaneous mutation rate because any colonies that grow on the control plate must have developed a reversion mutation - A chemical is a suspected mutagen if there are significantly more colonies on the experimental plate versus the control plate because the chemical induced reversion mutations at a significantly higher rate than the spontaneous background rate.
What is the function of the spliceosome, and what two types of molecule is the spliceosome composed of?
- The spliceosome performs splicing, in which introns are removed and exons are connected - The spliceosome is composed of multiple subunits, which are each composed of proteins and a type of functional RNA called small nuclear RNA (snRNA)
How many standard amino acids are there? What distinguishes the different amino acids?
- There are 20 standard amino acids distinguished by the side group - The side group gives each amino acid its distinct properties
What is the function of aminoacyl tRNA synthase enzymes?
- They add the correct amino acid to the correct tRNA molecule - A different aminoacyl tRNA synthase enzyme is required for each amino acid
Where does translation start and stop? Do the start and stop codons specify an amino acid?
- Translation starts at a methionine (Met) codon, which specifies the amino acid methionine (Met) - Translation stops at a Stop codon, which does not specify an amino acid
What is wobble between the codon and anticodon? In which position of the codon and anticodon is the wobble base located?
- Wobble means that the nucleotides located in the 3' position of the codon and the 5' position of the anticodon do not always base pair according to the complementary AU/GC base pairing rules - It enables one tRNA molecule to bind to more than one codon encoding the same amino acid
Define tautomeric shift
- a base changes structure to its other structural form
What is the difference between a focused promoter and a dispersed promoter? Do most human genes contain a focused promoter or a dispersed promoter?
- a focused promoter contains a consensus sequence such as the TATA box consensus sequence where the general transcription factors and RNA polymerase bind, then RNA polymerase initiates transcription from a defined transcriptional start site - a dispersed promoter does not contain a consensus sequence and contains several potential transcription initiation sites within a range of approx. 100 base pairs - it is currently not understood what determines the binding location of the general transcription factors and RNA polymerase for dispersed promoters - 30% of human genes are associated with focused promoter where 70% of human genes are associated with a dispersed promoter
What is a point mutation, and what causes point mutations?
- a mutation that affects a single base pair -caused by a base substitution event
What is an origin of replication? Does replication take place uni-directionally or bi-directionally from the origin?
- a site from which DNA replication is initiated - takes place bi-directionally from an origin of replication, therefore, there is a replication fork moving in each each direction
When is the enzyme telomerase active? When does telomerase cease being active in most somatic cells? What is senescence, and why do cells reach senescence?
- active during embryonic and fetal development - cease being active after birth - only remains active in certain cells types - telomeres gradually shorten each time cell division occurs - cells without active telomerase can divide a finite number if times and the reach senescence means cell division ceases - senescence occurs when telomere length becomes too short and the cells must stop diving so it doesn't lose germline DNA from the ends of chromosomes
What is the function of telomerase?
- adds telomere repeats to the 3' end of a parental (template) DNA strand - telomere repeats then get added to the 5' end of the complimentary daughter strand by DNA primase and DNA polymerase
When synthesizing the lagging strand, does DNA polymerase move toward the replication fork or away from the replication fork? In the lagging strand made continuously or as a series of okazaki fragments?
- away from the replication fork - moves opposite direction along the DNA strand though the strand bends around in space to keep DNA polymerase with the rest of the replication machinery
How is DNA replication initiated?
- by the sequential binding of several different proteins to the origin of replication - first, in the G1 of the cell cycle the origin of recognition complex (ORC) binds to the origin of replication on the template DNA strand - the ORC then recruits additional proteins to form the pre-initiation complex - in the S phase of the cell cycle the pre-replication complex is activated to form the pre-initiation complex by recruitment of additional factors including proteins that form the helicase complex - following formation of the pre-replication complex DNA polymerase and other components of the replication machinery are recruited to the origin
How could a transposable element cause a mutation?
- can cause mutation if it inserts into a gene or the regulatory sequences of the gene - can also promote structural changes to chromosomes if there is recombination between identical transposable element sequences at different chromosomal locations
What type of DNA damage does high-energy ionizing radiation (such as X-rays) cause?
- can react with molecules in cells to produce reactive oxygen species (ROS), which subsequently then react with DNA - can also directly cause DNA breaks which can result in mutation during the repair process
What is a nonsense mutation: i.e., does the mutation alter the codon sequence?
- caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon encodes a stop codon. The mutation causes early termination of translation resulting in a shortened polypeptide missing all amino acids encoded after the stop codon
What is a missense mutation: i.e., does the mutation alter the codon sequence?
- caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon is a non-synonymous codon that encodes a different amino acid
What is a silent mutation: i.e., does the mutation alter the codon sequence?
- caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon is a synonymous codon that encodes the same amino acid as the original codon
What is a frameshift mutation, and how does it occur?
- caused by the addition or deletion of a number of nucleotides not divisible by three - The added/deleted nucleotides alter the reading frame of the mRNA and change the codons that occur after the location of the addition/deletion
What does it mean when we say DNA replication is semi-conservative?
- each new strand in the existing DNA molecule (parent strand) serves as a template to produce a new strand (daughter strand) - after replication the new DNA molecules are composed of one original (parental) strand and one newly synthesized (daughter) strand - original DNA has been semi-conservative in each new strand
Explain how a base analog can result in a base substitution event during DNA replication.
- generally, base analogs do not follow the same base pairing rules as the base that they mimic, which results in a base substitution event during DNA replication
What is a consensus sequence? In the sequence below, what is the consensus sequence? GGC ATT GAC T GCC ATT GTC A CGC ATA GTC A GGA AAT GGG A GGC TTT GTC A GGC ATA GTC A
- lists the most common nucleotide at each position - GGC ATT CTC A
What is a tRNA anticodon sequence that brings each amino acid to the ribosome, and which amino acid does the tRNA carry? 3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3'
- mRNA: 5' - ACA GGG AUG AGG UCC CUU CUG ACC UAA AAC - 3 - tRNA anticodons: 3' - UAC UCC AGG GAA GAC UGG 5' - Amino acids: Met -Arg - Ser - Leu - Leu - Thr
Are transposable elements still capable of moving about the human genome?
- many are no longer capable of transposition, and several that are capable are silenced by host regulatory mechanisms - some transposable elements (LINEs and SINEs) continue to be able to move about the human genome at a low rate
What is the role of micro RNA (miRNA)? How can one micro RNA control the expression of many genes?
- miRNAs are a type of functional RNA molecule that binds to target mRNA and represses translation - miRNAs are typically 22 nucleotides long, but perfect complementarity need only be between the target mRNA - one miRNA can have many target mRNAs that all share the same short nucleotide sequence in the 3' UTR that is complementary to the seed region
DNA replication has a high fidelity. What accounts for the high fidelity?
- mismatched base pairing causes distortions of the DNA double helix - hydrogen bonding is less stable between mismatched base pairs and a mismatched base pair is less likely to be added versus a complementary base pair - if the wrong base is added DNA polymerase has proofreading activity and can digest DNA in the 3'-5' direction to remove the incorrect base
Does a silent mutation typically affect phenotype?
- not typically - it could affect phenotype if the base substitution occurs in a splice site (located at the exon/intron boundary regions) and subsequently causes aberrant splicing
Why is it necessary to make okazaki fragments on one strand?
- on the lagging strand DNA polymerase must synthesize the new strand in the 5'-3' direction but the replication fork is moving in the opposite direction along the strand - DNA polymerase must make a short okazaki fragment then move back towards the fork to make the next okazaki fragment once more template DNA has been separated
Why is DNA ligase needed to form the final phosphodiester bond to link okazaki fragments following removal of primers?
- once a primer has been removed the 5' DNA nucleotide that was linked to the primer only has one phosphate group therefore there is no pyrophosphate to provide energy for DNA polymerase to form a phosphodiester bond to link it to the 3' nucleotide of the upstream DNA fragment that replaced the primer - DNA ligase can make that phosphodiester bond to connect two adjacent DNA fragments
What is an RNA primer and why is it needed?
- short RNA sequence that is necessary to prime (begin) DNA replication - DNA polymerase cannot add a nucleotide to a bare strand, it needs a 3' end on which to add an incoming nucleotide
What are telomerase and why are they added? Does telomerase add telomere repeats to the 3' end or the 5' end of the template strand? After telomerase has added telomere repeats, how is the gap filled at the 5' end of the daughter strand?
- telomeres are found at the ends of chromosomes and are composed of a short DNA sequence repeated many times - they are added to prevent losing germline DNA from the ends of chromosomes during DNA replication - telomerase adds telomere repeats to the 3' end of a template DNA strand - DNA primase, polymerase, and ligase then synthesize a complementary sequence on the complementary daughter strand
What defines the origin of replication in higher eukaryotes, including human? Is the origin of replication defined by a specific sequence?
- there is not a defined consensus sequence that specifies origins of replication in human chromosomes - origin specification is determined by factors other than DNA sequence, but currently we do not know what brings the origin of recognition complex (ORC) to the sites that are used as origins in higher eukaryotes - there are thought to be frequent sites interspersed along chromosomes that can act as potential origins and only a subset of those potential sites are used with any round of DNA replication
When synthesizing the leading strand, does DNA polymerase move toward the replication fork or away from the replication fork? Is the leading strand made continuously or as a series of okazaki fragments?
- toward the replication fork - made as a continuous segment
Does the missense mutation alter the amino acid sequence?
- usually has a detrimental effect on the structure and function of the polypeptide (and resulting phenotype), but it does depend on the location of the amino acid substitution and the identity of the new amino acid - If the new amino acid is chemically/structurally like the original amino acid, and/or if the substitution occurs in a region of the protein that is not highly critical for folding or function, then there is a better chance the mutation will have a neutral rather than a detrimental effect
What are the 3 RNA modifications that happen to mRNA molecules, and what is the purpose of each of the events?
1. Addition of a 5' 7-methylguanosine cap: The 5' cap is required for export of the mRNA out of the nucleus, mRNA stability, and it is recognized by translation initiation factors that promote binding of the mRNA to the ribosome. 2. Addition of a 3' polyA tail: The polyA tail is required for export of the mRNA out of the nucleus and mRNA stability. It also interacts with translation initiation factors and promotes translation 3. Splicing: Splicing removes non-coding introns and connects exons.
describe the 3 stages of translation mentioning the roles of the A, P, and E sites.
1. Initiation: initiation factors bind to the 5' mRNA cap to facilitate binding of the mRNA to the 40S ribosomal subunit, and the first tRNA carrying Met binds to the P site. The complex then scans the mRNA for the start codon. After finding the start codon, the 60S ribosomal subunit associates with the small subunit. 2. Elongation: a tRNA with an anticodon complementary to the codon in the A site binds to the A site. A peptide bond forms between the amino acid in the A site and the amino acid at the end of the polypeptide chain held by the tRNA in the P site. The growing polypeptide chain is then transferred to the tRNA in the A site and the ribosome translocates one codon in the 3' direction. The tRNA in the E site exits the ribosome and a new tRNA comes into the A site for the cycle to start again 3. Termination: translation ends when there is a stop codon in the A site. The stop codon is recognized by a release factor which promotes release of the completed polypeptide and dissociation of the mRNA and ribosome subunits
Proteins have 3 or 4 levels of structure depending on whether the protein is composed on one or more than one polypeptide. Describe each of the 4 levels of protein structure.
1. Primary structure: Sequence of amino acids in the polypeptide 2. Secondary structure: polypeptide chain fold to form localized structures. Common structures are the alpha helix and beta sheet 3. Tertiary structure: The overall 3D folded shape of a polypeptide 4. Quaternary structure: two or more polypeptides to form a functional protein
Describe 3 ways in which activators and repressors act to affect gene expression.
1. Promote or inhibit the binding to TFIID to the promoter region. TFIID is the first GTF to bind to the promoter, and it then recruits other GTFs and RNA pol II 2. Interact with Mediator to promote or inhibit phosphorylation of the carboxyl terminal domain (CTD) of RNA pol II. Phosphorylation allows RNA pol II to begin elongation 3. Interact with chromatin remodeling complexes that alter chromatin structure to make the DNA either more accessible or less accessible to GTFs and RNA pol.
The Ames test was performed to determine whether chemical X is a likely mutagen. 1) On the control plate there were 5 colonies. On the experimental plate there were 6 colonies. Do the results indicate that chemical X is a mutagen? 2) What about if there were 5 colonies on the control plate and 50 colonies on the experimental plate?
1. The results do not indicate that chemical X is a mutagen because there is no substantial increase in the rate of reversion mutation on the experimental plate versus the control plate 2. The results indicate that chemical X is a likely mutagen as there is a substantial increase in the rate of reversion mutation on the experimental plate versus the control plate
What are the 3 mechanisms that a cell can use to regulate gene expression at the stage of transcription?
1. regulatory transcription factors 2. histone modifications 3. methylation of DNA
According to the original wobble rules, what is the minimum number of tRNAs needed to recognize all codons for Leucine (Leu)?
3
If a tRNA molecule carries glutamic acid, what are the two possible anticodon sequences that it could contain?
3' - CUU - 5' or 3' - CUC - 5'
Approximately how much off the human genome is composed of transposable element sequences?
45%
Consider the gene sequence below. 3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' Which DNA strand is the coding strand?
5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' - It contains a 5' - ATG - 3' sequence and a 5' - TAA - 3' sequence, which correspond to start and stop codons in mRNA
What is the mRNA sequence produced from this gene? 3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3'
5' - ACA GGG AUG AGG UCC CUU CUG ACC UAA AAC - 3'
If the DNA coding strand is 5' - ACG TAG CCA GGT - 3' what is the mRNA sequence transcribed?
5' - ACG UAG CCA GGU - 3'
A tRNA has the anticodon 5'-CCG-3'. Which mRNA codon(s) does this tRNA recognize? Which amino acid does this tRNA carry?
5' - CGG - 3' - The tRNA carries arginine (Arg) as specified by the codon
An mRNA codon has the sequence 5 - ACG - 3'. Which tRNA anticodon(s) will bind to this codon, and which amino acid does the tRNA carry?
5' - CGU - 3' or 5' - UGU - 3' - The tRNAs carry threonine (Thr) as specified by the codon.
If a tRNA has the anticodon sequence 3' - CCI - 5' which codon(s) can it recognize?
5' - GGU - 3', 5' - GGC - 3' and 5' - GGA - 3', which all encode glycine
A polypeptide contains 200 amino acids. How many nucleotides are in the coding sequence of the gene?
600
What is a CpG island?
A CpG island is a long stretches of CpG dinucleotide repeats, which is associated with approximately 70% of human promoters
It seems wasteful for organisms to use energy to transcribe introns only to remove them. What is an advantage of having genes that contain introns?
A genes can be alternatively spliced to produce different polypeptides by using different combinations of exons
What is a mutation?
A heritable change in DNA sequence
What is a trinucleotide repeat expansion (TNRE)?
A three nucleotide (trinucleotide) sequence expands in copy number
Below is a diagram of a chromosome. The end of each strand is labeled with A,B,C, or D. Which ends could not be replicated by DNA polymerase? Why not? 5' - A----------------------------------------------------------B - 3' 3' - C ---------------------------------------------------------D - 5'
B and C- the 3' ends of the template strands
How can a mutation in an intron sequence affect the resulting polypeptide?
If the mutation occurs in a splice site it may cause aberrant splicing of the mRNA resulting in exons inappropriately being spliced out or introns left in
What is the amino acid sequence encoded by the following mRNA? 3'- ACC AGU AUG UUU ACU UUA AUU UGA CGG GUA CAU CCG -5'
Met-Gly-Ser-Leu-Ile-Ser-Phe-Val
What is the amino acid sequence encoded by the following mRNA? 5' - GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA - 3'
Met-Gly-Ser-Leu-Ile-Ser-Phe-Val
Which base in DNA is methylated to affect gene expression?
Methyl groups can be added to cytosine (C) bases.
At what location in DNA does methylation of this base typically occur?
Methylation of cytosine bases typically occurs at CpG dinucleotide sequences
What are induced mutations?
Mutations caused by environmental agents: chemical agents or physical agents
Can mutations in germline cells be transmitted to offspring?
Mutations in germ-line cells can be transmitted to offspring
Can mutations in somatic cells be transmitted to offspring?
Mutations in somatic cells cannot be transmitted to offspring because only DNA in sperm cells and egg cells is transmitted to offspring.
Do all genes use the same DNA strand as the template strand?
No, different genes on the same chromosome can use a different DNA strand as the template strand but the same genes always has the same strand as the template strand
Explain how deamination and tautomeric shift result in a base substitution event during DNA replication.
The altered base does not follow the same base pairing rules as the original base during DNA replication, so a base substitution event will occur if the altered base is not repaired prior to DNA replication
How can translocations and inversions produce mutations that may affect phenotype?
The breakpoint that initiates the event may occur in a gene, or a gene may be moved to a new location where it is under the control of different regulatory elements that alter expression of the gene product
In the Ames test, explain why S. typhimurium His- mutants cannot grow in the absence of histidine.
The mutants have a mutation in a gene that is required for histidine synthesis
What is translation?
The sequence of nucleotides in mRNA directs the linking together of amino acids in a precise order to form a polypeptide
How does the spliceosome recognize introns?
The spliceosome recognizes the conserved intron branch site in the center of the intron and conserved 5' and 3' splice sites, which are located at exon/intron boundaries
What causes RNA polymerase to end transcription?
Transcription ends after RNA polymerase transcribes the polyA signal sequence. mRNA is cleaved shortly downstream of the polyA signal sequence.
Which physical agent, encountered every day, causes pyrimidine dimers?
Ultra violet (UV) light
What is a transversion mutation?
a pyrimidine base is replaced by a purine base or vice versa
What is a transition mutation?
a pyrimidine base is replaced by another pyrimidine base, or a purine base is replaced by another purine base
Define intercalating agent.
agents that have a planar structure, like the structure of DNA, and insert in between DNA bases.
Is the new DNA strand synthesized in the 5'-3' direction or the 3'-5' direction?
always synthesized in the 5'-3' direction and incoming nucleotides added to the 3' end
What is the function of single stranded binding proteins?
bind to single stranded DNA to protect DNA from degradation and to prevent the single strands reforming a double helix before replication has taken place
what type of mutations do intercalating agents cause?
can cause the insertion of bases into DNA or the deletion of bases from DNA.
Does DNA polymerase add nucleotides to the 5' end of the new strand or the 3' end of the new strand?
can only add nucleotides to the 3' end of a growing strand
Define base analog.
chemicals that are similar in structure to one of the DNA bases and can become incorporated instead of nucleotide during DNA replication.
Where does DNA polymerase get the energy for the formation of a phosphodiester bond?
cleavage of pyrophosphate from an incoming nucleotide triphosphate supplies the energy for phosphodiester bond formation
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - ACT - 3' to 5' - ACA - 3?
codon changes from ACU (Thr) to ACA (Thr) - silent mutation results
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - ACT - 3' to 5' - CCT - 3'?
codon changes from ACU (Thr) to CCU (Pro) - a missense mutation results
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - TAT - 3' to 5' - TAA - 3'?
codon changes from UAU (Tyr) to UAA (stop) - nonsense mutation results
What are DNA base tautomers?
different structural forms (isomers) of a base.
Does the silent mutation alter the amino acid sequence?
does not typically affect the structure and function of the polypeptide (and resulting phenotype) because the amino acid sequence is unchanged
If the DNA strand below acts as a template during DNA replication, which way will DNA polymerase slide along the strand from left to right or from right to left? 5' - ACTGGGCCTAGATTTAAC - 3'
from right to left because the new strand is made going from 5'-3' which is moving toward the right of the page
What is a germ line cell?
gametes and the lineage of cells that give rise to gametes
Does a nonsense mutation affect phenotype?
has a detrimental effect on phenotype
What is the function of DNA ligase?
it forms the final covalent bond to link the 5' nucleotide of one DNA fragment to the 3' nucleotide of the upstream DNA fragment which fills the gap after the primer was removed
Does a missense mutation affect phenotype?
it usually has a detrimental effect
What is the function of DNA primase?
lays down an RNA primer to prime (begin) replication
What is the function of DNA polymerase delta (δ)?
links together incoming nucleotides to synthesize the lagging strand
What is the function of DNA polymerase epsilon (ε)?
links together incoming nucleotides to synthesize the leading strand
What is the role of the mediator complex?
mediator interacts with regulatory transcription factors and regulated phosphorylation of the carboxyl terminal domain (CTD) of RNA pol II which is the switch between transcription initiation and elongation
What are transposable elements?
mobile genetic elements that can move about the genome (jumping genes)
Does the nonsense mutation alter the amino acid sequence?
mutation is expected to have a detrimental effect on polypeptide structure and function (and resulting phenotype)
Does the mutation alter amino acid sequence? Does the mutation affect phenotype?
mutation is expected to have a detrimental effect on protein structure and function (and resulting phenotype)
Does such a mutation of addition or deletion of a number of nucleotides divisible by three affect phenotype?
mutation is expected to have a neutral to detrimental effect on the structure and function of the polypeptide, but it does depend on the location of the mutation, the nature of the added/deleted amino acids, the number of amino acids added/deleted, and whether or not an existing codon was also disrupted
What are spontaneous mutations?
occur due to natural causes
What is a somatic cell?
other body cells that are not germ-line cells
What are reactive oxygen species (ROS)?
oxygen containing molecules that are highly reactive towards other molecules, including DNA
What is the function of DNA topoisomerase?
prevents supercoiling (tangling) of the DNA ahead of the replication fork
Define pyrimidine dimer.
refers to two adjacent pyrimidine bases that have are connected through chemical bonds
What is the function of flap endonuclease?
removes RNA primer by cleaving off RNA nucleotides from the 5' end
What is the function of DNA helicase complex?
separates the two DNA strands at the replication fork
What must occur for S. typhimurium His- to be able to grow in the absence of Histidine?
the bacteria must develop a reversion mutation that converts the mutant gene back to its original form
Define depurination
the loss of a purine base from DNA
Define the term deamination.
the loss of an amine group from a base
To which region of a gene does RNA polymerase bind to initiate transcription?
the promoter region
What happens during the process of transcription?
the sequence of DNA nucleotides in a gene is copied to a sequence of RNA nucleotides according to complimentary base pairing rules
What is the function of DNA polymerase alpha (α)?
works with DNA primase to initiate DNA replication from a primer
